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Sample GSM8124887 Query DataSets for GSM8124887
Status Public on Mar 05, 2024
Title H3K4me3_WT_GC_R1
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: GC Centrocytes
genotype: WT
treatment: Ab: Abcam ab8580
Treatment protocol Mice were immunized with sheep red blood cells (SRBC) 8 days before extraction of spleens
Extracted molecule genomic DNA
Extraction protocol Mint-ChIP was performed using H3K27Ac antibody (Cat#39133, lot 31814008) from Active Motif following the protocol from the Berstein lab. Briefly, 50,000 FACS sorted centrocytes, in triplicates, were processed with MNase to fragment native chromatin.
Barcoded adapters were ligated to every sample and samples were multiplexed for chromatin immunoprecipitation (ChIP). After ChIP, material was linearly amplified by RNA in vitro transcription in the presence of RNAse inhibitor RNAseOUT (Invitrogen 10777019). Fragments were reverse-transcribed and amplified as a library
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing The split reads were aligned using bwa mem to mm10. Duplicate marking and removal was done by Picard.
Peaking calling were preformed using two methods. The H3K4me1/H3K4me3 peaks were called against H3 total as input uisng Homer package with following command: findPeaks <H3K4Tag> -style histone 1000 -C 0 -o auto -i <H3_Tag>.
A consensus peaks were called using Genrich packages. All H3K4me1 and H3K4me3 aligned files are provided as sample and previously published H3 aligned files were provided as input to creat a concensus peak file.
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Normalized and scaled bigwigs and broadpeak or narrowpeak file
 
Submission date Mar 04, 2024
Last update date Mar 05, 2024
Contact name Christopher Russell Chin
E-mail(s) chc2077@med.cornell.edu
Phone 3393640514
Organization name Weill Cornell
Lab Melnick Lab
Street address 413 E 69th Street, Belfer Building, BB-1462
City New York City
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL19057
Series (2)
GSE224513 Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas.
GSE260811 Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas [Mint-ChIP]
Relations
BioSample SAMN40253465
SRA SRX23829062

Supplementary file Size Download File type/resource
GSM8124887_H3K4me3_WT_GC_R1_fc.bw 384 b (ftp)(http) BW
GSM8124887_H3K4me3_WT_GC_R1_peaks.broadPeak.gz 1.1 Mb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA

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